Update bundled GDCM version from 3.2.1 to 3.2.2

Modules/ThirdParty/GDCM/UpdateFromUpstream.sh

@@ -8,7 +8,7 @@ readonly name="GDCM"
 readonly ownership="GDCM Upstream <gdcm-developers@lists.sourceforge.net>"
 readonly subtree="Modules/ThirdParty/GDCM/src/gdcm"
 readonly repo="https://github.com/malaterre/GDCM.git"
-readonly tag="v3.2.1"
+readonly tag="v3.2.2"
 readonly shortlog=false
 readonly paths="
   .gitattributes

Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt

@@ -10,7 +10,7 @@ endif()
 #----------------------------------------------------------------------------
 
 project(GDCM
-  VERSION 3.2.1
+  VERSION 3.2.2
   LANGUAGES CXX C
 )
 ## NOTE: the "DESCRIPTION" feature of project() was introduced in cmake 3.10.0

Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmSequenceOfFragments.h

@@ -237,7 +237,7 @@ std::istream& ReadValue(std::istream &is, bool /*readvalues*/)
       const size_t lastf = Fragments.size() - 1;
       const ByteValue *bv = Fragments[ lastf ].GetByteValue();
       const char *a = bv->GetPointer();
-      gdcmAssertAlwaysMacro( (unsigned char)a[ bv->GetLength() - 3 ] == 0xfe );
+      gdcmAssertAlwaysMacro( bv->GetLength() >= 3 && (unsigned char)a[ bv->GetLength() - 3 ] == 0xfe );
       Fragments[ lastf ].SetByteValue( bv->GetPointer(), bv->GetLength() - 3 );
       is.seekg( -11, std::ios::cur );
       gdcm_assert( is.good() );

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmPixelFormat.cxx

@@ -278,6 +278,11 @@ bool PixelFormat::Validate()
     gdcmDebugMacro( "Bits Stored is 0. Setting is to max value" );
     BitsStored = BitsAllocated;
     }
+  if ( HighBit == 0 && BitsStored > 1 )
+    {
+    gdcmDebugMacro( "High Bit is 0. Setting is to BitStored - 1" );
+    HighBit = BitsStored - 1;
+    }
   if ( BitsAllocated == 24 )
     {
     gdcmDebugMacro( "ACR-NEMA way of storing RGB data. Updating" );

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmPixelFormat.h

@@ -165,7 +165,9 @@ class GDCM_EXPORT PixelFormat
       case 0x0ffe: hb = 11; break;
       case 0x00fe: hb =  7; break;
       }
-    if( hb < BitsStored )
+    if( BitsStored > 1 && hb == 0 )
+      HighBit = BitsStored - 1;
+    else if( hb < BitsStored )
       HighBit = hb;
     }
 

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmSplitMosaicFilter.cxx

@@ -16,6 +16,7 @@
 #include "gdcmAttribute.h"
 #include "gdcmImageHelper.h"
 #include "gdcmDirectionCosines.h"
+#include "gdcmEquipmentManufacturer.h"
 
 #include <cmath>
 
@@ -120,14 +121,57 @@ bool SplitMosaicFilter::GetAcquisitionSize(unsigned int size[2], DataSet const &
   return found;
 }
 
+const DataElement& ComputeCSAHeaderInfo(const DataSet& ds, const PrivateTag &pt, const Tag &hardcodedCsaLocation, bool handleMissingPrivateCreator ) {
+  if ( handleMissingPrivateCreator && !ds.FindDataElement(pt) ) {
+    // check hardcoded location first:
+    if ( ds.FindDataElement(hardcodedCsaLocation) ) {
+      Attribute<0x0008, 0x0008> imageType;
+      imageType.SetFromDataSet(ds);
+      const unsigned int nvalues = imageType.GetNumberOfValues();
+      const std::string str4 = nvalues >= 5 ? imageType.GetValue(4).Trim() : "";
+      const char mosaic[] = "MOSAIC";
+      if ( str4 == mosaic ) {
+        gdcmWarningMacro( "CSAImageHeaderInfo private creator missing. Using hardcoded location (0029,1010)" );
+        return ds.GetDataElement(hardcodedCsaLocation);
+      }
+      const EquipmentManufacturer::Type manufacturer = EquipmentManufacturer::Compute(ds);
+      if ( manufacturer == EquipmentManufacturer::SIEMENS ) {
+        gdcmWarningMacro( "CSAImageHeaderInfo private creator missing. Using hardcoded location (0029,1010)" );
+        return ds.GetDataElement(hardcodedCsaLocation);
+      }
+    }
+  }
+  return ds.GetDataElement(pt);
+}
+
+// For some reason anoymizer from ADNI DICOM remove the private creator for SIEMENS CSA
+// Since dcm2niix has a hardcoded location for SIEMENS CSA tag 0029,1010 we want to reproduce
+// the behavior for the average user.
+// ref: LEVEY^ADNI3 Basic / Axial rsfMRI (Eyes Open)
+// (0029,1008) CS [IMAGE NUM 4]                            #  12, 1 Unknown Tag & Data
+// (0029,1010) OB 53\56\31\30\04\03\02\01\65\00\00\00\4d\00\00\00\45\63\68\6f\4c\69... # 13012, 1 Unknown Tag & Data
+// (0029,1018) CS [MR]                                     #   2, 1 Unknown Tag & Data
+// (0029,1020) OB 53\56\31\30\04\03\02\01\4f\00\00\00\4d\00\00\00\55\73\65\64\50\61... # 132968, 1 Unknown Tag & Data
+const DataElement& SplitMosaicFilter::ComputeCSAImageHeaderInfo(const DataSet& ds, const bool handleMissingPrivateCreator ) {
+  const PrivateTag &pt = CSAHeader::GetCSAImageHeaderInfoTag();
+  const Tag hardcodedCsaLocation(0x0029,0x1010);
+  return ComputeCSAHeaderInfo(ds, pt, hardcodedCsaLocation, handleMissingPrivateCreator);
+}
+
+const DataElement& SplitMosaicFilter::ComputeCSASeriesHeaderInfo(const DataSet& ds, const bool handleMissingPrivateCreator ) {
+  const PrivateTag &pt = CSAHeader::GetCSASeriesHeaderInfoTag();
+  const Tag hardcodedCsaLocation(0x0029,0x1020);
+  return ComputeCSAHeaderInfo(ds, pt, hardcodedCsaLocation, handleMissingPrivateCreator);
+}
+
 unsigned int SplitMosaicFilter::GetNumberOfImagesInMosaic( File const & file )
 {
   unsigned int numberOfImagesInMosaic = 0;
   DataSet const &ds = file.GetDataSet();
   CSAHeader csa;
 
-  const PrivateTag &t1 = csa.GetCSAImageHeaderInfoTag();
-  if( csa.LoadFromDataElement( ds.GetDataElement( t1 ) ) )
+  const DataElement& csaEl = ComputeCSAImageHeaderInfo( ds ) ;
+  if( csa.LoadFromDataElement( csaEl ) )
   {
     if( csa.FindCSAElementByName( "NumberOfImagesInMosaic" ) )
     {
@@ -234,9 +278,9 @@ bool SplitMosaicFilter::ComputeMOSAICSliceNormal( double slicenormalvector[3], b
 
   double normal[3];
   bool snvfound = false;
-  const PrivateTag &t1 = csa.GetCSAImageHeaderInfoTag();
   static const char snvstr[] = "SliceNormalVector";
-  if( csa.LoadFromDataElement( ds.GetDataElement( t1 ) ) )
+  const DataElement& csaEl = ComputeCSAImageHeaderInfo( ds ) ;
+  if( csa.LoadFromDataElement( csaEl ) )
   {
     if( csa.FindCSAElementByName( snvstr ) )
     {

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmSplitMosaicFilter.h

@@ -81,6 +81,12 @@ class GDCM_EXPORT SplitMosaicFilter
 
   /// Return the value for NumberOfImagesInMosaic, or compute it from Acquisition Size
   static unsigned int GetNumberOfImagesInMosaic( File const & file );
+
+  /// Return the DataElement for the CSA Image Header
+  static const DataElement& ComputeCSAImageHeaderInfo(const DataSet& ds, bool handleMissingPrivateCreator = true);
+
+  /// Return the DataElement for the CSA Series Header
+  static const DataElement& ComputeCSASeriesHeaderInfo(const DataSet& ds, bool handleMissingPrivateCreator = true);
 
 protected: